Comparison of SARS-CoV-2 RT-PCR on a high-throughput molecular diagnostic platform and the cobas SARS-CoV-2 test for the diagnostic of COVID-19 on various clinical samples

Abstract

Objectives: In order to cope with the rapid spread of the COVID-19 pandemic, we introduced on our in-house high-throughput molecular diagnostic platform (MDx Platform) a real-time reverse transcriptase PCR (RT-PCR) to detect the SARS-CoV-2 from any clinical specimens. The aim of this study was to compare the RT-PCR results obtain with the MDx Platform and the commercial assay cobas SARS-CoV-2 (Roche) on nasopharyngeal swab and other clinical specimens including sputum, bronchial aspirate, bronchoalveolar lavage and anal swabs.

Methods: Samples received in our laboratory from patients suspected of COVID-19 (n = 262) were tested in parallel with our MDx platform SARS-CoV-2 PCR and with the cobas SARS-CoV-2 test.

Results: The overall agreement between the two tests for all samples tested was 99.24% (260/262), which corresponded to agreements of 100% (178/178) on nasopharyngeal swabs, 95.45% (42/44) on lower respiratory tract specimen with discordant resultS obtained for very high cycle threshold (Ct) value and 100% (40/40) on anorectal swabs. The Ct values for nasopharyngeal swabs displayed an excellent correlation (R2 > 96%) between both tests.

Conclusions: The high agreements between the cobas SARS-CoV-2 test and the MDx platform supports the use of both methods for the diagnostic of COVID-19 on various clinical samples. Very few discrepant results may occur at very low viral load.

Keywords: COVID-19; RT-PCR, molecular diagnostic; SARS-CoV-2; anal swab; anorectal swab; bronchial aspirate; bronchoalveolar lavage; cobas 6800; nasopharyngeal swab.

Figure 1.

SARS-CoV-2 detection using our in-house automated molecular diagnostic platform and the cobas the SARS-CoV-2 test in our laboratory. (A) Use of the in-house automated molecular diagnostic platform (blue) and the cobas the SARS-CoV-2 test (orange) during the course of the epidemic; the area represent the number of tests achieved per days while the dash line represent the results validated. Indeed, in some cases the analysis run started at J0 just before midnight and was validated at J+1. (B) Cycle threshold (Ct) values of the molecular diagnostic platform and of the cobas SARS-CoV-2 test. (C) Median of the Ct value of the molecular diagnostic platform and of the cobas SARS-CoV-2 test obtained for positive results (n = 55) (D) Bland–Altman graphic showing the (difference versus average) to compare the Ct value of the molecular diagnostic platform and of the cobas SARS-CoV-2 test.